chr19-44157679-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006630.3(ZNF234):c.1663C>T(p.Leu555Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000093 in 1,613,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
ZNF234
NM_006630.3 missense
NM_006630.3 missense
Scores
6
9
Clinical Significance
Conservation
PhyloP100: 4.51
Genes affected
ZNF234 (HGNC:13027): (zinc finger protein 234) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.25803876).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF234 | NM_006630.3 | c.1663C>T | p.Leu555Phe | missense_variant | 6/6 | ENST00000426739.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF234 | ENST00000426739.7 | c.1663C>T | p.Leu555Phe | missense_variant | 6/6 | 1 | NM_006630.3 | P1 | |
ZNF234 | ENST00000592437.5 | c.1663C>T | p.Leu555Phe | missense_variant | 6/6 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151538Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250796Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135788
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GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461894Hom.: 0 Cov.: 40 AF XY: 0.00000825 AC XY: 6AN XY: 727248
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151538Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 73966
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.1663C>T (p.L555F) alteration is located in exon 6 (coding exon 4) of the ZNF234 gene. This alteration results from a C to T substitution at nucleotide position 1663, causing the leucine (L) at amino acid position 555 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MutPred
Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP
MPC
0.53
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at